Cargando…

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells

BACKGROUND: Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Acetylation of specific lysine residues of histones plays a key role in regulating gene expres...

Descripción completa

Detalles Bibliográficos
Autores principales: Karmodiya, Krishanpal, Krebs, Arnaud R, Oulad-Abdelghani, Mustapha, Kimura, Hiroshi, Tora, Laszlo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473242/
https://www.ncbi.nlm.nih.gov/pubmed/22920947
http://dx.doi.org/10.1186/1471-2164-13-424
_version_ 1782246732701106176
author Karmodiya, Krishanpal
Krebs, Arnaud R
Oulad-Abdelghani, Mustapha
Kimura, Hiroshi
Tora, Laszlo
author_facet Karmodiya, Krishanpal
Krebs, Arnaud R
Oulad-Abdelghani, Mustapha
Kimura, Hiroshi
Tora, Laszlo
author_sort Karmodiya, Krishanpal
collection PubMed
description BACKGROUND: Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Acetylation of specific lysine residues of histones plays a key role in regulating gene expression. RESULTS: Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse embryonic stem (mES) cells. Genome-wide H3K9ac and H3K14ac show very high correlation between each other as well as with other histone marks (such as H3K4me3) suggesting a coordinated regulation of active histone marks. Moreover, the levels of H3K9ac and H3K14ac directly correlate with the CpG content of the promoters attesting the importance of sequences underlying the specifically modified nucleosomes. Our data provide evidence that H3K9ac and H3K14ac are also present over the previously described bivalent promoters, along with H3K4me3 and H3K27me3. Furthermore, like H3K27ac, H3K9ac and H3K14ac can also differentiate active enhancers from inactive ones. Although, H3K9ac and H3K14ac, a hallmark of gene activation exhibit remarkable correlation over active and bivalent promoters as well as distal regulatory elements, a subset of inactive promoters is selectively enriched for H3K14ac. CONCLUSIONS: Our study suggests that chromatin modifications, such as H3K9ac and H3K14ac, are part of the active promoter state, are present over bivalent promoters and active enhancers and that the extent of H3K9 and H3K14 acetylation could be driven by cis regulatory elements such as CpG content at promoters. Our study also suggests that a subset of inactive promoters is selectively and specifically enriched for H3K14ac. This observation suggests that histone acetyl transferases (HATs) prime inactive genes by H3K14ac for stimuli dependent activation. In conclusion our study demonstrates a wider role for H3K9ac and H3K14ac in gene regulation than originally thought.
format Online
Article
Text
id pubmed-3473242
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-34732422012-10-18 H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells Karmodiya, Krishanpal Krebs, Arnaud R Oulad-Abdelghani, Mustapha Kimura, Hiroshi Tora, Laszlo BMC Genomics Research Article BACKGROUND: Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Acetylation of specific lysine residues of histones plays a key role in regulating gene expression. RESULTS: Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse embryonic stem (mES) cells. Genome-wide H3K9ac and H3K14ac show very high correlation between each other as well as with other histone marks (such as H3K4me3) suggesting a coordinated regulation of active histone marks. Moreover, the levels of H3K9ac and H3K14ac directly correlate with the CpG content of the promoters attesting the importance of sequences underlying the specifically modified nucleosomes. Our data provide evidence that H3K9ac and H3K14ac are also present over the previously described bivalent promoters, along with H3K4me3 and H3K27me3. Furthermore, like H3K27ac, H3K9ac and H3K14ac can also differentiate active enhancers from inactive ones. Although, H3K9ac and H3K14ac, a hallmark of gene activation exhibit remarkable correlation over active and bivalent promoters as well as distal regulatory elements, a subset of inactive promoters is selectively enriched for H3K14ac. CONCLUSIONS: Our study suggests that chromatin modifications, such as H3K9ac and H3K14ac, are part of the active promoter state, are present over bivalent promoters and active enhancers and that the extent of H3K9 and H3K14 acetylation could be driven by cis regulatory elements such as CpG content at promoters. Our study also suggests that a subset of inactive promoters is selectively and specifically enriched for H3K14ac. This observation suggests that histone acetyl transferases (HATs) prime inactive genes by H3K14ac for stimuli dependent activation. In conclusion our study demonstrates a wider role for H3K9ac and H3K14ac in gene regulation than originally thought. BioMed Central 2012-08-24 /pmc/articles/PMC3473242/ /pubmed/22920947 http://dx.doi.org/10.1186/1471-2164-13-424 Text en Copyright ©2012 Karmodiya et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Karmodiya, Krishanpal
Krebs, Arnaud R
Oulad-Abdelghani, Mustapha
Kimura, Hiroshi
Tora, Laszlo
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
title H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
title_full H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
title_fullStr H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
title_full_unstemmed H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
title_short H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
title_sort h3k9 and h3k14 acetylation co-occur at many gene regulatory elements, while h3k14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473242/
https://www.ncbi.nlm.nih.gov/pubmed/22920947
http://dx.doi.org/10.1186/1471-2164-13-424
work_keys_str_mv AT karmodiyakrishanpal h3k9andh3k14acetylationcooccuratmanygeneregulatoryelementswhileh3k14acmarksasubsetofinactiveinduciblepromotersinmouseembryonicstemcells
AT krebsarnaudr h3k9andh3k14acetylationcooccuratmanygeneregulatoryelementswhileh3k14acmarksasubsetofinactiveinduciblepromotersinmouseembryonicstemcells
AT ouladabdelghanimustapha h3k9andh3k14acetylationcooccuratmanygeneregulatoryelementswhileh3k14acmarksasubsetofinactiveinduciblepromotersinmouseembryonicstemcells
AT kimurahiroshi h3k9andh3k14acetylationcooccuratmanygeneregulatoryelementswhileh3k14acmarksasubsetofinactiveinduciblepromotersinmouseembryonicstemcells
AT toralaszlo h3k9andh3k14acetylationcooccuratmanygeneregulatoryelementswhileh3k14acmarksasubsetofinactiveinduciblepromotersinmouseembryonicstemcells